[English] 日本語
Yorodumi
- PDB-6sbj: X-ray structure of mus musculus Fumarylacetoacetate hydrolase dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sbj
TitleX-ray structure of mus musculus Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) apo-form uuncomplexed
ComponentsAcylpyruvase FAHD1, mitochondrial
KeywordsHYDROLASE
Function / homology
Function and homology information


acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / oxaloacetate tautomerase / oxaloacetate tautomerase activity / acetylpyruvate hydrolase activity / Pyruvate metabolism / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / oxaloacetate metabolic process ...acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / oxaloacetate tautomerase / oxaloacetate tautomerase activity / acetylpyruvate hydrolase activity / Pyruvate metabolism / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / oxaloacetate metabolic process / pyruvate metabolic process / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetate (FAA) hydrolase C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Oxaloacetate tautomerase FAHD1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsRupp, B. / Naschberger, A. / Weiss, A.K.H.
Funding support Austria, 2items
OrganizationGrant numberCountry
European Commission512020 Austria
Austrian Science FundP28395-B26 Austria
CitationJournal: Biosci.Rep. / Year: 2020
Title: Structural and functional comparison of fumarylacetoacetate domain containing protein 1 in human and mouse.
Authors: Weiss, A.K.H. / Naschberger, A. / Cappuccio, E. / Metzger, C. / Mottes, L. / Holzknecht, M. / von Velsen, J. / Bowler, M.W. / Rupp, B. / Jansen-Durr, P.
History
DepositionJul 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acylpyruvase FAHD1, mitochondrial
B: Acylpyruvase FAHD1, mitochondrial
C: Acylpyruvase FAHD1, mitochondrial
D: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,01116
Polymers117,6524
Non-polymers35912
Water2,072115
1
A: Acylpyruvase FAHD1, mitochondrial
B: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0058
Polymers58,8262
Non-polymers1796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-76 kcal/mol
Surface area16660 Å2
MethodPISA
2
C: Acylpyruvase FAHD1, mitochondrial
D: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0058
Polymers58,8262
Non-polymers1796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-74 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.401, 69.959, 107.557
Angle α, β, γ (deg.)90.000, 92.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRARGARGAA10 - 22448 - 262
21THRTHRARGARGBB10 - 22448 - 262
12PROPROSERSERAA12 - 22550 - 263
22PROPROSERSERCC12 - 22550 - 263
13LYSLYSSERSERAA11 - 22549 - 263
23LYSLYSSERSERDD11 - 22549 - 263
14PROPROARGARGBB12 - 22450 - 262
24PROPROARGARGCC12 - 22450 - 262
15LYSLYSARGARGBB11 - 22449 - 262
25LYSLYSARGARGDD11 - 22449 - 262
16PROPROARGARGCC12 - 22450 - 262
26PROPROARGARGDD12 - 22450 - 262

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Acylpyruvase FAHD1, mitochondrial / Fumarylacetoacetate hydrolase domain-containing protein 1 / Oxaloacetate decarboxylase / OAA decarboxylase


Mass: 29412.994 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fahd1, MNCb-4134 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8R0F8, acylpyruvate hydrolase, oxaloacetate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 27 % / Description: thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% (w/v) PEG 3350, 0.2 M MgCl2 and 0.1 M Bis/Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 20, 2018
RadiationMonochromator: Diamond C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.217→42.65 Å / Num. obs: 26144 / % possible obs: 89.2 % / Redundancy: 3.44 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.963 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.159 / Rrim(I) all: 0.298 / Net I/σ(I): 4.6
Reflection shellResolution: 2.217→2.466 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1316 / CC1/2: 0.553 / Rpim(I) all: 0.609 / Rrim(I) all: 1.138 / % possible all: 45.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOH

6foh


Resolution: 2.22→42.65 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / SU ML: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.521 / SU Rfree Cruickshank DPI: 0.341
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1219 4.7 %RANDOM
Rwork0.1933 ---
obs0.1962 24929 67.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.31 Å2 / Biso mean: 27.656 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.56 Å2
2---0.02 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 2.22→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 12 115 6576
Biso mean--22.85 13.23 -
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176449
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.6329007
X-RAY DIFFRACTIONr_angle_other_deg1.2221.57615010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1295833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69621.796284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.104151189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6391538
X-RAY DIFFRACTIONr_chiral_restr0.0660.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021318
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A63580.1
12B63580.1
21A62470.1
22C62470.1
31A62610.1
32D62610.1
41B62730.08
42C62730.08
51B63020.08
52D63020.08
61C62670.08
62D62670.08
LS refinement shellResolution: 2.22→2.273 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.345 3 -
Rwork0.265 142 -
obs--5.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32980.0398-0.10660.1442-0.12480.1577-0.02080.03720.00050.00770.00930.0218-0.01410.01880.01150.07720.0023-0.02580.0578-0.00620.112123.32943.047842.3992
20.26780.01180.0830.1553-0.10690.1618-0.0082-0.02930.01440.00370.00790.0205-0.00140.0020.00020.0724-0.0046-0.01430.0601-0.00810.12066.2583-3.127962.1109
30.6217-0.2879-0.09450.218-0.31841.9043-0.13130.04790.0880.00650.0719-0.05920.1396-0.34150.05940.1021-0.0811-0.0080.1546-0.01870.01719.6358-26.0628-8.7037
40.30010.03730.23570.3046-0.53791.2997-0.0704-0.0479-0.06010.0338-0.0009-0.0922-0.0983-0.10640.07140.07510.0001-0.04580.07710.03120.078816.3816-25.441717.3087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 225
2X-RAY DIFFRACTION2B5 - 225
3X-RAY DIFFRACTION3C12 - 225
4X-RAY DIFFRACTION4D11 - 225

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more